RyR modelling for heart failure prevention

Heart failure is a leading cause of death in the world. Calcium is believed to be the
key molecule for the maintenance of cardiac function. During a heart cycle, calcium is
released from the sarcoplasmic reticulum (SR) through calcium channels - called
ryanodine receptors (RyRs) - into the cytoplasm of cardiac muscle cells. That increase
of calcium concentration triggers muscle contraction. Then, muscle relaxation
happens when calcium returns to SR. Recent research shows that perturbation of that
mechanism produces human heart failure. Consequently, RyRs appear like a prime
target for drugs. RyRs are homo tetramers constructed from a subunit of molecular
mass 565 Kda. 3D structures of those macro molecules exist and were generated using
3D cryo-microscopy. However, their low resolution (~24 angstrom) does not allow a
deep understanding of mechanisms involved in those calcium channels and limits
their usefulness for rational drug design.
The aim of this research project is the generation of atomic resolution models of RyRs
and the analysis of those channels functioning. Although amino acid sequences of
RyRs are available, atomic modelling of those ion channels has not been possible
using standard Bioinformatics techniques including homology modelling, threading
and molecular dynamics. RyRs complexity is particularly high because they are the
largest known ion channels and they contain around 10 protein domains. We want to
design a novel methodology which would allow tackling that challenging problem. It
would rely on our combined Bioinformatics and Biomedical Engineering expertise,
which includes modelling atomic protein binding site [1] and functioning of RyRs [2]
ion channel.
The general principle is to produce a collection of models of RyRs complementing
standard structure modelling techniques with indirect and partial structural
information. Then comparison of the known channel behaviour with a channel
simulation, using each of the new RyRs model, will be used to select, refine and
validate the models. This process is iterated with the production of models of
increased resolution. Available structural information includes 3D cryo-microscopy
models [3], atomic 3D structures of binding sites of proteins binding RyRs, e.g.
FKBP12.6 [3] and calsequestrin [4], and the recent structure of calmoduline binding a
fragment of a RyR [5]. Moreover, a systematic analysis of consequences of known
mutations in RyRs would provide cues regarding the possible 3D location of specific
residues. This structural information would be combined with detection of sequence
patterns and secondary structure prediction. Our models would permit a better
understanding of those ion channels by allowing testing some hypothesis such as the
putative role of the FKBP12.6 protein in coupling channel gating between adjacent
RyRs. Moreover, they should contribute to the design of novel drugs for heart failure
patients.
[1] Nebel J.-C., Generation of 3D templates of active sites of proteins with rigid prosthetic groups,
Bioinformatics, 22(10):1183-1189, 2006.
[2] Kania M., Kotulska M., A system for modeling the cooperativity of ryanodine receptors in cardiac
myocytes, Proc. IFMBE European Conference on Biomedical Engineering, EMBEC'05, 2005.
[3] Sharma M.R., Jeyakumar L.H., Fleischer S., Wagenknecht T., 3D visualization of FKBP12.6
binding to an open conformation of cardiac ryanodine receptor, Biophys J., 90(1):164-72, 2006.
[4] Park H., Park I.Y., Kim E., Youn B., Fields K., Dunker A.K., Kang C., Comparing skeletal and
cardiac calsequestrin structures and their calcium binding: a proposed mechanism for coupled calcium
binding and protein polymerization, J Biol Chem., 279(17):18026-33, 2004.
[5] Maximciuc A., Putkey J., Shamoo Y., MacKenzie K., Complex of Calmodulin with a Ryanodine
Receptor Target Reveals a Novel, Flexible Binding Mode, Structure, 14(10):1547-1556,2006.